Coral reef calcification: carbonate,bicarbonate and proton flux under conditions of increasing ocean acidification

Data on calcification rate of coral and crustose coralline algae were used to test the proton flux model of calcification. There was a significant correlation between calcification (G) and the ratio of dissolved inorganic carbon (DIC) to proton concentration ([DIC] : [H⁺] ratio). The ratio is tightly correlated with [CO₃²⁻] and with aragonite saturation state (Ω_a). An argument is presented that correlation does not prove cause and effect, and that Ω_a and [CO₃²⁻] have no basic physiological meaning on coral reefs other than a correlation with [DIC] : [H⁺] ratio, which is the driver of G.     

Simultaneous fingerprint and high‐wavenumber fiber‐optic Raman spectroscopy enhances real‐time in vivo diagnosis of adenomatous polyps during colonoscopy

Colorectal cancer can be prevented if detected early (e.g., precancerous polyps‐adenoma). Endoscopic differential diagnosis of hyperplastic polyps (that have little or no risk of malignant transformation) and adenomas (that have prominent malignant latency) remains an unambiguous clinical challenge. Raman spectroscopy is an optical vibrational technique capable of probing biomolecular changes of tissue associated with neoplastic transformation. This work aims to apply a fiber‐optic simultaneous fingerprint (FP) and high wavenumber (HW) Raman spectroscopy technique for real‐time in vivo assessment of adenomatous polyps during clinical colonoscopy. We have developed a fiber‐optic Raman endoscopic technique capable of simultaneously acquiring both the FP (i.e., 800–1800 cm^–1) and HW (i.e., 2800–3600 cm^–1) Raman spectra from colorectal tissue subsurface (<200 µm) for real‐time assessment of colorectal carcinogenesis. In vivo FP/HW Raman spectra were acquired from 50 patients with 17 colorectal polyps during clinical colonoscopy. Prominent Raman spectral differences (p < 0.001) were found between hyperplastic (n = 118 spectra), adenoma (n = 184 spectra) that could be attributed to changes in inter‐ and intra‐cellular proteins, lipids, DNA and water structures and conformations. Simultaneous FP/HW Raman endoscopy provides a diagnostic sensitivity of 90.9% and specificity of 83.3% for differentiating adenoma from hyperplastic polyps, which is superior to either the FP or HW Raman technique alone. This study shows that simultaneous FP/HW Raman spectroscopy technique has the potential to be a clinically powerful tool for improving early diagnosis of adenomatous polyps in vivo during colonoscopic examination.

     

Unshelled abalone and corrupted urchins: development of marine calcifiers in a changing ocean

The most fragile skeletons produced by benthic marine calcifiers are those that larvae and juveniles make to support their bodies. Ocean warming, acidification, decreased carbonate saturation and their interactive effects are likely to impair skeletogenesis. Failure to produce skeleton in a changing ocean has negative implications for a diversity of marine species. We examined the interactive effects of warming and acidification on an abalone (Haliotis coccoradiata) and a sea urchin (Heliocidaris erythrogramma) reared from fertilization in temperature and pH/pCO(2) treatments in a climatically and regionally relevant setting. Exposure of ectodermal (abalone) and mesodermal (echinoid) calcifying systems to warming (+2°C to 4°C) and acidification (pH 7.6-7.8) resulted in unshelled larvae and abnormal juveniles. Haliotis development was most sensitive with no interaction between stressors. For Heliocidaris, the percentage of normal juveniles decreased in response to both stressors, although a +2°C warming diminished the negative effect of low pH. The number of spines produced decreased with increasing acidification/pCO(2), and the interactive effect between stressors indicated that a +2°C warming reduced the negative effects of low pH. At +4°C, the developmental thermal tolerance was breached. Our results show that projected near-future climate change will have deleterious effects on development with differences in vulnerability in the two species.     

Slow‐flow habitats as refugia for coastal calcifiers from ocean acidification

The pH of the oceans’ surface water is dropping, termed ocean acidification (OA), and the 0.4 unit reduction in pH by 2100 is projected to negatively impact benthic coastal organisms that produce calcium carbonate “skeletons.” Research has focussed on identifying species that are susceptible to OA, but there is an urgent need to discover refuge habitats that will afford protection to vulnerable species. The susceptibility of calcium carbonate skeletons to dissolution by OA depends on the pH at their surface, and this is controlled by the interaction between seawater velocity and organismal metabolism. This perspective considers how seawater velocity modifies the responses of calcifying organisms (seaweed, shellfish, and tropical corals) to OA through its action on controlling diffusion boundary layer thickness and thereby the pH and calcium carbonate saturation state (Ω) at the organisms’ surface. Evidence is presented to support the idea that slow‐flow habitats, such as wave‐sheltered bays or the within canopies of seaweed/seagrass beds, might provide inexpensive refugia from OA for vulnerable coastal calcifiers.     

Real‐time endoscopic Raman spectroscopy for in vivo early lung cancer detection

Currently the most sensitive method for localizing lung cancers in central airways is autofluorescence bronchoscopy (AFB) in combination with white light bronchoscopy (WLB). The diagnostic accuracy of WLB + AFB for high grade dysplasia (HGD) and carcinoma in situ is variable depending on physician's experience. When WLB + AFB are operated at high diagnostic sensitivity, the associated diagnostic specificity is low. Raman spectroscopy probes molecular vibrations and gives highly specific, fingerprint‐like spectral features and has high accuracy for tissue pathology classification. In this study we present the use of a real‐time endoscopy Raman spectroscopy system to improve the specificity. A spectrum is acquired within 1 second and clinical data are obtained from 280 tissue sites (72 HGDs/malignant lesions, 208 benign lesions/normal sites) in 80 patients. Using multivariate analyses and waveband selection methods on the Raman spectra, we have demonstrated that HGD and malignant lung lesions can be detected with high sensitivity (90%) and good specificity (65%).

     

Combined effects of ocean acidification and solar UV radiation on photosynthesis,growth, pigmentation and calcification of the coralline alga Corallina sessilis (Rhodophyta)

Previous studies have shown that increasing atmospheric CO₂ concentrations affect calcification in some planktonic and macroalgal calcifiers due to the changed carbonate chemistry of seawater. However, little is known regarding how calcifying algae respond to solar UV radiation (UVR, UVA+UVB, 280–400 nm). UVR may act synergistically, antagonistically or independently with ocean acidification (high CO₂/low pH of seawater) to affect their calcification processes. We cultured the articulated coralline alga Corallina sessilis Yendo at 380 ppmv (low) and 1000 ppmv (high) CO₂ levels while exposing the alga to solar radiation treatments with or without UVR. The presence of UVR inhibited the growth, photosynthetic O₂ evolution and calcification rates by13%, 6% and 3% in the low and by 47%, 20% and 8% in the high CO₂ concentrations, respectively, reflecting a synergistic effect of CO₂ enrichment with UVR. UVR induced significant decline of pH in the CO₂‐enriched cultures. The contents of key photosynthetic pigments, chlorophyll a and phycobiliproteins decreased, while UV‐absorptivity increased under the high pCO₂/low pH condition. Nevertheless, UV‐induced inhibition of photosynthesis increased when the ratio of particulate inorganic carbon/particulate organic carbon decreased under the influence of CO₂‐acidified seawater, suggesting that the calcified layer played a UV‐protective role. Both UVA and UVB negatively impacted photosynthesis and calcification, but the inhibition caused by UVB was about 2.5–2.6 times that caused by UVA. The results imply that coralline algae suffer from more damage caused by UVB as they calcify less and less with progressing ocean acidification.     

Determination of inclusion depth in ex vivo animal tissues using surface enhanced deep Raman spectroscopy

This work presents recent developments in spatially offset and transmission Raman spectroscopy for noninvasive detection and depth prediction of a single SERS inclusion located deep inside ex vivo biological tissues. The concept exploits the differential attenuation of Raman bands brought about by their different absorption due to tissue constituents enabling to predict the inclusion depth. Four different calibration models are tested and evaluated to predict the depth of surface enhanced Raman scattering labelled nanoparticles, within an up to 40 mm slab of porcine tissue. An external measurement carried out in transmission mode, with a noninvasively built model on the analysed sample, is shown to be insensitive to variations of the overall thickness of the tissue yielding an average root‐mean‐square error of prediction of 6.7%. The results pave the way for future noninvasive deep Raman spectroscopy in vivo enabling to localise cancer biomarkers for an early diagnosis of multiple diseases.      

Coralline algae (Rhodophyta) in a changing world: integrating ecological,physiological, and geochemical responses to global change

Coralline algae are globally distributed benthic primary producers that secrete calcium carbonate skeletons. In the context of ocean acidification, they have received much recent attention due to the potential vulnerability of their high‐Mg calcite skeletons and their many important ecological roles. Herein, we summarize what is known about coralline algal ecology and physiology, providing context to understand their responses to global climate change. We review the impacts of these changes, including ocean acidification, rising temperatures, and pollution, on coralline algal growth and calcification. We also assess the ongoing use of coralline algae as marine climate proxies via calibration of skeletal morphology and geochemistry to environmental conditions. Finally, we indicate critical gaps in our understanding of coralline algal calcification and physiology and highlight key areas for future research. These include analytical areas that recently have become more accessible, such as resolving phylogenetic relationships at all taxonomic ranks, elucidating the genes regulating algal photosynthesis and calcification, and calibrating skeletal geochemical metrics, as well as research directions that are broadly applicable to global change ecology, such as the importance of community‐scale and long‐term experiments in stress response.     

Shifts in coralline algae,macroalgae, and coral juveniles in the Great Barrier Reef associated with present‐day ocean acidification

Seawater acidification from increasing CO₂ is often enhanced in coastal waters due to elevated nutrients and sedimentation. Our understanding of the effects of ocean and coastal acidification on present‐day ecosystems is limited. Here we use data from three independent large‐scale reef monitoring programs to assess coral reef responses associated with changes in mean aragonite saturation state (Ω_ar) in the Great Barrier Reef World Heritage Area (GBR). Spatial declines in mean Ω_ar are associated with monotonic declines in crustose coralline algae (up to 3.1‐fold) and coral juvenile densities (1.3‐fold), while non‐calcifying macroalgae greatly increase (up to 3.2‐fold), additionally to their natural changes across and along the GBR. These three key groups of organisms are important proxies for coral reef health. Our data suggest a tipping point at Ω_ar 3.5–3.6 for these coral reef health indicators. Suspended sediments acted as an additive stressor. The latter suggests that effective water quality management to reduce suspended sediments might locally and temporarily reduce the pressure from ocean acidification on these organisms.     

Cell classification with low‐resolution Raman spectroscopy (LRRS)

The identification of individual eukaryotic and prokaryotic cells is the backbone of clinical pathology and provides crucial information about the genesis and progression of a disease. While most commonly fluorescent‐label based methods are applied, label‐free methods, such as Raman spectroscopy, are elegant alternatives. A major disadvantage of Raman spectroscopy is the low signal yield resulting in long acquisition times, making it impractical for high‐throughput clinical analysis. As a rule, Raman‐based cell identification relies on high‐resolution Raman spectra. This comes at a cost of detected Raman photons. In this letter we show that while the proper biochemical characterization of cells requires high‐resolution Raman spectra, the proper classification of cells does not. By varying the slit‐width between 50 µm and 500 µm it is possible to show that detected Raman signal from eukaryotic cells increased up to seven‐fold. Raman‐based cell classification was performed on three cancer cell lines: Jurkat, MiaPaca2, and Capan1, at three different resolutions 8 cm^–1, 24 cm^–1, and 48 cm^–1. Moreover, we have simulated the resolution decrease due to low‐diffraction gratings by binning neighboring pixels together. In both cases the cells were well classifiable using support vectors machine (SVM).

For anyone working in the field of Raman spectroscopy this picture of Sir C.V. Raman is recognizable, even with reduced spatial resolution. Raman spectra of eukaryotic cells can also be recognized even with six fold reduced spectral resolution.     

Multiple phases of mg‐calcite in crustose coralline algae suggest caution for temperature proxy and ocean acidification assessment: lessons from the ultrastructure and biomineralization in Phymatolithon (Rhodophyta,Corallinales)1

Magnesium content, strongly correlated with temperature, has been developed as a climate archive for the late Holocene without considering anatomical controls on Mg content. In this paper, we explore the ultrastructure and cellular scale Mg‐content variations within four species of North Atlantic crust‐forming Phymatolithon. The cell wall has radial grains of Mg‐calcite, whereas the interfilament (middle lamella) has grains aligned parallel to the filament axis. The proportion of interfilament and cell wall carbonate varies by tissue and species. Three distinct primary phases of Mg‐calcite were identified: interfilament Mg‐calcite (mean 8.9 mol% MgCO₃), perithallial cell walls Mg‐calcite (mean 13.4 mol% MgCO₃), and hypothallium Mg‐calcite (mean 17.1 mol% MgCO₃). Magnesium content for the bulk crust, an average of all phases present, showed a strongly correlated (R² = 0.975) increase of 0.31 mol% MgCO₃ per °C. Of concern for climate reconstructions is the potential for false warming signals from undetected postgrazing wound repair carbonate that is substantially enriched in Mg, unrelated to temperature. Within a single crust, Mg‐content of component carbonates ranged from 8 to 20 mol% MgCO₃, representing theoretical thermodynamic stabilities from aragonite‐equivalent to unstable higher‐Mg‐calcite. It is unlikely that existing current predictions of ocean acidification impact on coralline algae, based on saturation states calculated using average Mg contents, provide an environmentally relevant estimate.     

Linking genotype to phenotype in a changing ocean: inferring the genomic architecture of a blue mussel stress response with genome‐wide association

A key component to understanding the evolutionary response to a changing climate is linking underlying genetic variation to phenotypic variation in stress response. Here, we use a genome‐wide association approach (GWAS) to understand the genetic architecture of calcification rates under simulated climate stress. We take advantage of the genomic gradient across the blue mussel hybrid zone (Mytilus edulis and Mytilus trossulus) in the Gulf of Maine (GOM) to link genetic variation with variance in calcification rates in response to simulated climate change. Falling calcium carbonate saturation states are predicted to negatively impact many marine organisms that build calcium carbonate shells – like blue mussels. We sampled wild mussels and measured net calcification phenotypes after exposing mussels to a ‘climate change’ common garden, where we raised temperature by 3°C, decreased pH by 0.2 units and limited food supply by filtering out planktonic particles >5 μm, compared to ambient GOM conditions in the summer. This climate change exposure greatly increased phenotypic variation in net calcification rates compared to ambient conditions. We then used regression models to link the phenotypic variation with over 170 000 single nucleotide polymorphism loci (SNPs) generated by genotype by sequencing to identify genomic locations associated with calcification phenotype, and estimate heritability and architecture of the trait. We identified at least one of potentially 2–10 genomic regions responsible for 30% of the phenotypic variation in calcification rates that are potential targets of natural selection by climate change. Our simulations suggest a power of 13.7% with our study's average effective sample size of 118 individuals and rare alleles, but a power of >90% when effective sample size is 900.     

Identification and characterization of bladder cancer by low‐resolution fiber‐optic Raman spectroscopy

Raman spectroscopy has been proved to be a promising diagnostic technique for various cancers detection. A major drawback for its clinical translation is the intrinsic weakness of Raman effects. Highly sensitive equipment and optimal measurement conditions are generally applied to overcome this drawback. However, these equipment are usually bulky, expensive and may also be easily influenced by surrounding environment. In this preliminary work, a low‐resolution fiber‐optic Raman sensing system is applied to evaluate the diagnostic potential of Raman spectroscopy to identify different bladder pathologies ex vivo. A total number of 262 spectra taken from 32 bladder specimens are included in this study. These spectra are categorized into 3 groups by histopathological analysis, namely normal bladder tissues, low‐grade bladder tumors and high‐grade bladder tumors. Principal component analysis fed artificial neural network are used to train a classification model for the spectral data with 10‐fold cross‐validation and an overall prediction accuracy of 93.1% is obtained. The sensitivities and specificities for normal bladder tissues, low‐grade bladder tumors and high‐grade bladder tumors are 88.5% and 95.1%, 90.3% and 98%, and 97.5% and 96.4%, respectively. These results demonstrate the potential of using a low‐resolution fiber‐optic Raman system for in vivo bladder cancer diagnosis.      

Productivity gains do not compensate for reduced calcification under near‐future ocean acidification in the photosynthetic benthic foraminifer species Marginopora vertebralis

Changes in the seawater carbonate chemistry (ocean acidification) from increasing atmospheric carbon dioxide (CO₂) concentrations negatively affect many marine calcifying organisms, but may benefit primary producers under dissolved inorganic carbon (DIC) limitation. To improve predictions of the ecological effects of ocean acidification, the net gains and losses between the processes of photosynthesis and calcification need to be studied jointly on physiological and population levels. We studied productivity, respiration, and abundances of the symbiont‐bearing foraminifer species Marginopora vertebralis on natural CO₂ seeps in Papua New Guinea and conducted additional studies on production and calcification on the Great Barrier Reef (GBR) using artificially enhanced pCO₂. Net oxygen production increased up to 90% with increasing pCO₂; temperature, light, and pH together explaining 61% of the variance in production. Production increased with increasing light and increasing pCO₂ and declined at higher temperatures. Respiration was also significantly elevated (~25%), whereas calcification was reduced (16–39%) at low pH/high pCO₂ compared to present‐day conditions. In the field, M. vertebralis was absent at three CO₂ seep sites at pH_Total levels below ~7.9 (pCO₂ ~700 μatm), but it was found in densities of over 1000 m^?2 at all three control sites. The study showed that endosymbiotic algae in foraminifera benefit from increased DIC availability and may be naturally carbon limited. The observed reduction in calcification may have been caused either by increased energy demands for proton pumping (measured as elevated rates of respiration) or by stronger competition for DIC from the more productive symbionts. The net outcome of these two competing processes is that M. vertebralis cannot maintain populations under pCO₂ exceeding 700 μatm, thus are likely to be extinct in the next century.     

Acclimation to ocean acidification during long‐term CO2 exposure in the cold‐water coral Lophelia pertusa

Ocean acidity has increased by 30% since preindustrial times due to the uptake of anthropogenic CO₂ and is projected to rise by another 120% before 2100 if CO₂ emissions continue at current rates. Ocean acidification is expected to have wide‐ranging impacts on marine life, including reduced growth and net erosion of coral reefs. Our present understanding of the impacts of ocean acidification on marine life, however, relies heavily on results from short‐term CO₂ perturbation studies. Here, we present results from the first long‐term CO₂ perturbation study on the dominant reef‐building cold‐water coral Lophelia pertusa and relate them to results from a short‐term study to compare the effect of exposure time on the coral's responses. Short‐term (1 week) high CO₂ exposure resulted in a decline of calcification by 26–29% for a pH decrease of 0.1 units and net dissolution of calcium carbonate. In contrast, L. pertusa was capable to acclimate to acidified conditions in long‐term (6 months) incubations, leading to even slightly enhanced rates of calcification. Net growth is sustained even in waters sub‐saturated with respect to aragonite. Acclimation to seawater acidification did not cause a measurable increase in metabolic rates. This is the first evidence of successful acclimation in a coral species to ocean acidification, emphasizing the general need for long‐term incubations in ocean acidification research. To conclude on the sensitivity of cold‐water coral reefs to future ocean acidification further ecophysiological studies are necessary which should also encompass the role of food availability and rising temperatures.     

Autofluorescence and white light imaging‐guided endoscopic Raman and diffuse reflectance spectroscopy for in vivo nasopharyngeal cancer detection

Nasopharyngeal cancer (NPC) is an endemic with high incidence in Southern China and Southeast Asia countries. Screening for NPC under conventional white light imaging (WLI) nasopharyngoscope examination remains a great clinical challenge due to its poor sensitivity. Here, we developed an integrated 4‐modality endoscopy system combining WLI, autofluorescence imaging (AFI), diffuse reflectance spectroscopy and Raman spectroscopy technologies for in vivo endoscopic cancer detection for the first time. A pilot clinical test of the system for NPC detection was conducted, in which 283 in vivo Raman and diffuse reflectance spectral data sets from 30 NPC patients and 30 healthy subjects were acquired under the guidance of AFI and WLI. Both high diagnostic sensitivity (98.6%) and high specificity (95.1%) for differentiating cancer from normal tissue sites were achieved using this system combined with principal component analysis‐linear discriminant analysis diagnostic algorithm, demonstrating great potential for improving real‐time, in vivo diagnosis of NPC at endoscopy.      

Raman spectroscopy as a non‐invasive technique for the quantification of melanins in feathers and hairs

The quantification of melanins is a complex task due to the chemical heterogeneity of the pigments and the difficulty of their isolation. The best accepted procedure currently consists in the chemical cleavage of melanins and the subsequent detection of degradation products by HPLC, which implies the destruction of samples. Here, we show that Raman spectroscopy is a non‐invasive technique that can be used to quantify melanins. We made parallel analyses of the characteristics of pheomelanin and eumelanin Raman spectra as measured by confocal Raman microscopy and of degradation products of pheomelanin (4‐amino‐3‐hydroxyphenylalanine, 4‐AHP) and eumelanin (pyrrole‐2,3,5‐tricarboxylic acid, PTCA) as measured by HPLC in feathers of red‐legged partridges and hairs of wild boars and humans. We found strong correlations between the spectral Raman characteristics and 4‐AHP and PTCA levels, which indicates that the Raman spectra of melanins can be used to determine their content.     

Raman spectroscopy provides a powerful,rapid diagnostic tool for the detection of tuberculous meningitis in ex vivo cerebrospinal fluid samples

In this letter, we propose a novel method for diagnosis of tuberculous meningitis using Raman spectroscopy. The silicate Raman signature obtained from Mycobacterium tuberculosis positive cases enables specific and sensitive detection of tuberculous meningitis from acquired cerebrospinal fluid samples. The association of silicates with the tuberculosis mycobacterium is discussed. We envision that this new method will facilitate rapid diagnosis of tuberculous meningitis without application of exogenous reagents or dyes and can be aptly used as a complementary screening tool to the existing gold standard methods. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Calcification is not the Achilles’ heel of cold‐water corals in an acidifying ocean

Ocean acidification is thought to be a major threat to coral reefs: laboratory evidence and CO₂ seep research has shown adverse effects on many coral species, although a few are resilient. There are concerns that cold‐water corals are even more vulnerable as they live in areas where aragonite saturation (Ω_ara) is lower than in the tropics and is falling rapidly due to CO₂ emissions. Here, we provide laboratory evidence that net (gross calcification minus dissolution) and gross calcification rates of three common cold‐water corals, Caryophyllia smithii, Dendrophyllia cornigera, and Desmophyllum dianthus, are not affected by pCO₂ levels expected for 2100 (pCO₂ 1058 μatm, Ω_ara 1.29), and nor are the rates of skeletal dissolution in D. dianthus. We transplanted D. dianthus to 350 m depth (pH_T 8.02; pCO₂ 448 μatm, Ω_ara 2.58) and to a 3 m depth CO₂ seep in oligotrophic waters (pH_T 7.35; pCO₂ 2879 μatm, Ω_ara 0.76) and found that the transplants calcified at the same rates regardless of the pCO₂ confirming their resilience to acidification, but at significantly lower rates than corals that were fed in aquaria. Our combination of field and laboratory evidence suggests that ocean acidification will not disrupt cold‐water coral calcification although falling aragonite levels may affect other organismal physiological and/or reef community processes.     

A comparative evaluation of diffuse reflectance and Raman spectroscopy in the detection of cervical cancer

Optical spectroscopic techniques show improved diagnostic accuracy for non‐invasive detection of cervical cancers. In this study, sensitivity and specificity of two in vivo modalities, i.e diffuse reflectance spectroscopy (DRS) and Raman spectroscopy (RS), were compared by utilizing spectra recorded from the same sites (67 tumor (T), 22 normal cervix (C), and 57 normal vagina (V)). Data was analysed using principal component – linear discriminant analysis (PC‐LDA), and validated using leave‐one‐out‐cross‐validation (LOOCV). Sensitivity, specificity, positive predictive value and negative predictive value for classification between normal (N) and tumor (T) sites were 91%, 96%, 95% and 93%, respectively for RS and 85%, 95%, 93% and 88%, respectively for DRS. Even though DRS revealed slightly lower diagnostic accuracies, owing to its lower cost and portability, it was found to be more suited for cervical cancer screening in low resource settings. On the other hand, RS based devices could be ideal for screening patients with centralised facilities in developing countries.